Dear Gromacs users I am facing a strange problem while doing pdb2gmx:- When I use the command:- gmx pdb2gmx -f 74A-G.pdb -o 74A-G.gro It shows the following:- going to rename ./amber99sb-ildn.ff/aminoacids.r2b Opening force field file ./amber99sb-ildn.ff/aminoacids.r2b going to rename ./amber99sb-ildn.ff/dna.r2b Opening force field file ./amber99sb-ildn.ff/dna.r2b going to rename ./amber99sb-ildn.ff/rna.r2b Opening force field file ./amber99sb-ildn.ff/rna.r2b Reading 74A-G.pdb... Read '', 4082 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 492 residues with 4082 atoms
chain #res #atoms 1 'A' 489 3970 2 'B' 3 112 All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp ------------------------------------------------------- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: Invalid atomtype format: '' However, when I use without gmx, as below:- pdb2gmx -f 74A-G.pdb -o 74A-G.gro It generates topology file successfully. What's wrong with the format in atomtypes.atp I am unable to understand. Could you please help me to find out? I have added a new residue to my forcefield file as mentioned in gromacs manual. Please correct me where I am wrong, I have added following in atomtypes.atp file:- ;[ atomtypes ] ; name bond_type mass charge ptype sigma eps nh 14.01000 0.000 A 3.25000e-1 7.11280e-1 hn 1.00800 0.000 A 1.06908e-1 6.56888e-2 ca 12.01000 0.000 A 3.39967e-1 3.59824e-1 nb 14.01000 0.000 A 3.25000e-1 7.11280e-1 h5 1.00800 0.000 A 2.42146e-1 6.27600e-2 nc 14.01000 0.000 A 3.25000e-1 7.11280e-1 cd 12.01000 0.000 A 3.39967e-1 3.59824e-1 na 14.01000 0.000 A 3.25000e-1 7.11280e-1 c3 12.01000 0.000 A 3.39967e-1 4.57730e-1 h2 1.00800 0.000 A 2.29317e-1 6.56888e-2 os 16.00000 0.000 A 3.00001e-1 7.11280e-1 h1 1.00800 0.000 A 2.47135e-1 6.56888e-2 p5 30.97000 0.000 A 3.74177e-1 8.36800e-1 o 16.00000 0.000 A 2.95992e-1 8.78640e-1 oh 16.00000 0.000 A 3.06647e-1 8.80314e-1 ho 1.00800 0.000 A 0.00000e+0 0.00000e+0 h4 1.00800 0.000 A 2.51055e-1 6.27600e-2 c 12.01000 0.000 A 3.39967e-1 3.59824e-1 n 14.01000 0.000 A 3.25000e-1 7.11280e-1 ha 1.00800 0.000 A 2.59964e-1 6.27600e-2 Thanks. Sadaf -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.